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HomeMy WebLinkAboutSuWa207sec9-14Alaska Resources Library & Information Services Susitna-Watana Hydroelectric Project Document ARLIS Uniform Cover Page Title: Genetic baseline study for selected fish species, Study plan Section 9.14 : Initial study report SuWa 207 Author(s) – Personal: Author(s) – Corporate: Prepared by Gene Conservation Laboratory, Commercial Fisheries Division, Alaska Department of Fish and Game AEA-identified category, if specified: Draft initial study report AEA-identified series, if specified: Series (ARLIS-assigned report number): Susitna-Watana Hydroelectric Project document number 207 Existing numbers on document: Published by: [Anchorage : Alaska Energy Authority, 2014] Date published: February 2014 Published for: Alaska Energy Authority Date or date range of report: Volume and/or Part numbers: Study plan Section 9.14 Final or Draft status, as indicated: Draft Document type: Pagination: vi, 40, 2 p. Related work(s): Pages added/changed by ARLIS: Notes: All reports in the Susitna-Watana Hydroelectric Project Document series include an ARLIS- produced cover page and an ARLIS-assigned number for uniformity and citability. All reports are posted online at http://www.arlis.org/resources/susitna-watana/ Susitna-Watana Hydroelectric Project (FERC No. 14241) Genetic Baseline Study for Selected Fish Species Study Plan Section 9.14 Initial Study Report Prepared for Alaska Energy Authority Prepared by Gene Conservation Laboratory Commercial Fisheries Division Alaska Department of Fish and Game February 2014 Draft INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page i February 2014 Draft TABLE OF CONTENTS Executive Summary ...................................................................................................................... v 1. Introduction ....................................................................................................................... 1 2. Study Objectives................................................................................................................ 2 3. Study Area ......................................................................................................................... 2 4. Methods ............................................................................................................................. 2 4.1. Sample Collection ................................................................................................... 3 4.1.1. Adult Chinook salmon collections .................................................. 3 4.1.2. Other adult salmon collections........................................................ 5 4.1.3. Juvenile Chinook salmon collections.............................................. 5 4.1.4. Other species collections................................................................. 6 4.1.5. Sampling coordination with other studies....................................... 7 4.1.6. Collection trip documentation......................................................... 7 4.2. Tissue Storage ......................................................................................................... 7 4.3. Laboratory Analysis ................................................................................................ 8 4.4. Data Retrieval and Quality Control ........................................................................ 8 4.5. Variances from Study Plan ..................................................................................... 8 5. Results ................................................................................................................................ 8 5.1. Sample Collection ................................................................................................... 8 5.1.1. Adult Chinook salmon collections .................................................. 8 5.1.2. Other adult salmon collections........................................................ 9 5.1.3. Juvenile Chinook salmon collections.............................................. 9 5.1.4. Other species collections................................................................. 9 5.1.5. Pacific salmon sampling coordination with other studies............... 9 5.1.6. Collection trip documentation....................................................... 10 5.2. Tissue Storage ....................................................................................................... 10 5.3. Laboratory Analysis .............................................................................................. 10 5.4. Data Retrieval and Quality Control ...................................................................... 10 6. Discussion......................................................................................................................... 10 6.1. Chinook Salmon Adults and Juveniles Above Devils Canyon ............................. 10 6.2. Chinook Salmon Adults in the Middle River Below Devils Canyon ................... 11 6.3. Chinook Salmon Adults Elsewhere ...................................................................... 11 INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page ii February 2014 Draft 6.4. Chinook Salmon Juveniles – Lower River ........................................................... 11 6.5. Other Salmon Adults............................................................................................. 12 6.6. Other Fish Species ................................................................................................ 12 6.7. Coordination with Other Studies .......................................................................... 12 7. Literature Cited .............................................................................................................. 13 8. Tables ............................................................................................................................... 14 9. Figures .............................................................................................................................. 34 LIST OF TABLES Table 4-1. Area, location, and sublocation of baseline samples of adult and juvenile Chinook salmon spawning aggregates for genetic analysis. ..................................................15 Table 4-2. Location and sublocation of baseline samples of adult sockeye salmon spawning aggregates for genetic analysis. .............................................................................20 Table 4-3. Location and sublocation of baseline samples of adult chum salmon spawning aggregates for genetic analysis. .............................................................................................22 Table 4-4. Location and sublocation of baseline samples of adult coho salmon spawning aggregates for genetic analysis. .............................................................................................24 Table 4-5. Location and sublocation of baseline samples of adult pink salmon spawning aggregates for genetic analysis. .............................................................................................26 Table 4-6. Resident and non-salmon anadromous fish species targeted for genetic tissue sampling in the Susitna River and samples sizes collected in 2013. .....................................28 Table 4-7. Summary of survey flights conducted during 2013. ....................................................30 Table 4-8. Genetic sampling effort through time by river area for adult salmon species in 2013. .......................................................................................................................................31 Table 4-9. Juvenile Chinook salmon tissue collections across five habitat types in the Lower Susitna River, through September 15, 2013. ..............................................................32 Table 4-10. Metadata and location of Chinook salmon samples collected above Devils Canyon. ..................................................................................................................................33 INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page iii February 2014 Draft LIST OF FIGURES Figure 2-1. A generalized flow chart to distinguish among hypotheses of population structure for Chinook salmon collected over spawning habitat above Devils Canyon in the Middle and Upper Susitna River. .................................................................................34 Figure 3-1. Collection strata for samples collected for genetic archive and/or analysis. ..............35 Figure 4-1. Baseline sampling locations for adult sockeye salmon. .............................................36 Figure 4-2. Baseline sampling locations for adult chum salmon. .................................................37 Figure 4-3. Baseline sampling locations for adult coho salmon. ..................................................38 Figure 4-4. Baseline sampling locations for adult pink salmon. ...................................................39 Figure 4-5. Baseline sampling locations for adult and juvenile (inset) Chinook salmon. ............40 APPENDICES Appendix A. Template for collection trip reports. INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page iv February 2014 Draft LIST OF ACRONYMS, ABBREVIATIONS, AND DEFINITIONS Abbreviation Definition ADF&G Alaska Department of Fish and Game AEA Alaska Energy Authority CFR Code of Federal Regulations CIRWG Cook Inlet Region Working Group DNA deoxyribonucleic acid FERC Federal Energy Regulatory Commission GCL Gene Conservation Laboratory GPS global positioning system ILP Integrated Licensing Process IP Implementation Plan ISR Initial Study Report ml milliliter Mm Millimeter MSA mixed-stock analyses n/a not applicable/not available NOAA National Oceanic and Atmospheric Administration NMFS National Marine Fisheries Service oz. ounce PRM Project River Mile Project Susitna-Watana Hydroelectric Project RM River Mile(s) referencing those of the 1980s Project. RSP Revised Study Plan SPD Study Plan Determination USFWS United States Fish and Wildlife Service INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page v February 2014 Draft EXECUTIVE SUMMARY Genetic Baseline Study for Selected Fish Species 9.14 Purpose The purpose of this study is to collect tissue samples suitable for genetic analyses from Susitna River fish species, conduct genetic analysis of Chinook salmon, and establish tissue repositories for all four other salmon species and 20 non-salmon fish species. Chinook salmon tissue will be used to characterize genetic population structure, examine genetic variation for use in mixed-stock analysis, and, if sufficient variation is found, estimate the contribution of Chinook salmon originating upstream of Devils Canyon to select habitats in the Lower River. Salmon and non-salmon tissue repositories will be used for future studies to characterize the genetic legacy and variation of species and populations of interest. Status Field collections began in 2012, were expanded in 2013, and will be completed in a final year of study. Chinook salmon analysis began in the fourth quarter of 2013. Collections are on target to meet sampling goals over the 2-year study with two exceptions: 1) odd-year pink salmon were not found spawning in the Chulitna River and were therefore not collected and 2) Chinook salmon from selected tributaries above or near Devils Canyon were not accessible which may impede temporal analyses (Section 4.5). Study Components Salmon tissue samples were collected via targeted fieldwork conducted by this study. Non-salmon tissue samples were provided via opportunistic collections from this and four other studies conducted for the Project. Sampling dates, sample sizes, and locations targeted by this study vary based on species and study component, but in total represent the most species-comprehensive genetic collections from fresh waters in northern Cook Inlet. All samples were delivered to the Gene Conservation Laboratory operated by the Alaska Department of Fish and Game. Thereafter, some samples were archived for future use and Chinook salmon collections underwent preliminary analysis for genetic variation and mixed stock analysis. 2013 Variances AEA implemented the methods as described in the Study Plan with the exception of the following variances. The significance of these variances is discussed within the ISR. In 2013, there were no variances from the collection, storage and analysis methods described in the Study Plan; however, full access to all of the sampling sites was not available in 2013. Access was not available to collect Chinook salmon samples in tributaries flowing through Cook Inlet Regional Working Group (CIRWG) lands above or near Devils Canyon (Cheechako, Devil, Fog, Tsusena and Watana creeks) in 2013. Lack of land access prevented sampling of coho salmon from Portage and Prairie creeks, and reduced sampling effort for sockeye salmon in Prairie Creek (Genetics IP Section 4.2; see ISR Section 4.5). INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page vi February 2014 Draft Genetic Baseline Study for Selected Fish Species 9.14 Steps to Complete the Study As explained in the cover letter to this draft ISR, AEA’s plan for completing this study will be included in the final ISR filed with FERC on June 3, 2014. Highlighted Results and Achievements The study made excellent progress towards tissue collections of Susitna River fish species in 2013, with over 4,500 samples collected representing the most species-comprehensive genetic collections from fresh waters in northern Cook Inlet. INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 1 February 2014 Draft 1. INTRODUCTION On December 14, 2012, Alaska Energy Authority (AEA) filed its Revised Study Plan (RSP) with the Federal Energy Regulatory Commission (FERC or Commission) for the Susitna-Watana Hydroelectric Project (FERC Project No. 14241) which included 58 individual study plans (AEA 2012). Included within the RSP was the Genetic Baseline Study for Selected Fish Species, Section 9.14. RSP Section 9.14 focuses on understanding the genetic structure of selected species within the Susitna River. On February 1, 2013, FERC staff issued its study determination (February 1 SPD) for 44 of the 58 studies, approving 31 studies as filed and 13 with modifications. RSP Section 9.14 was one of the 13 approved with modifications. In its February 1 SPD, FERC recommended the following: AEA consult with the FWS and NMFS prior to preparing the project operational plans; distribute draft project operational plans to the agencies by March 31 of each year of study implementation; allow 15 days for the agencies to provide comments on the draft plans; file the final plans with the Commission by April 30 of each year of study implementation; and include with the final plans, documentation of agency consultation, a description of how agency comments are incorporated into the final plans, and an explanation for why any agency comments are not incorporated into the final plans. To the extent feasible, we recommend that AEA collect tissue samples over a representative proportion of the entire adult Chinook salmon run. We recommend that AEA include in the 2013 project operational plan, a schedule for when the 2012 genetics studies would be available, and include provisions for filing those results with the Commission through either the initial study report, or a supplemental report in 2013. We also recommend that the report on the 2012 preliminary genetics studies clearly describe the criteria, using current scientific literature, to determine whether there is sufficient genetic uniqueness to estimate the percentage of Chinook originating from Upper and Middle River habitats in areas sampled downstream. Finally, we recommend that the report on the 2012 preliminary genetics studies clearly describe whether the study results indicate that sufficient genetic uniqueness is found to characterize the presence and relative proportion of fish originating from the Upper and Middle River in selected Lower River habitats as described in section 9.14.4.7 of the study plan. In accordance with the February 1 SPD, AEA provided a draft 2013 Implementation Plan for the Genetic Baseline Study for Selected Fish Species in the Susitna River, Alaska (Genetics Implementation Plan [IP]) for review on March 31, 2013 and filed a final 2013 Genetics IP on April 30, 2013. The 2013 Genetics IP supersedes portions of the Revised Study Plan. In accordance with the February 1 SPD, AEA has adopted the FERC requested modifications. Following the first study season, FERC’s regulations for the Integrated Licensing Process (ILP) require AEA to “prepare and file with the Commission an initial study report describing its INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 2 February 2014 Draft overall progress in implementing the study plan and schedule and the data collected, including an explanation of any variance from the study plan and schedule.” (18 CFR 5.15(c)(1)) This Initial Study Report (ISR) on Genetic Baseline Study has been prepared in accordance with FERC’s ILP regulations and details AEA’s status in implementing the study, as set forth in the FERC- approved RSP and as modified by FERC’s February 1 SPD and the 2013 Implementation Plan (collectively referred to herein as the “Study Plan”). 2. STUDY OBJECTIVES The goals of this study are to (1) acquire genetic material from samples of selected fish species within the Susitna River drainage, (2) characterize the genetic structure of Chinook salmon in the Susitna River watershed and (3) assess the use of Lower and Middle River habitat by juvenile Chinook salmon originating in the Middle and Upper Susitna River. As described in the 2013 Genetics IP Section 3, the objectives of this study are to: 1. Develop a repository of genetic samples for target resident fish species captured within the Lower, Middle, and Upper Susitna River drainage. 2. Contribute to the development of genetic baselines for chum, coho, pink, and sockeye salmon spawning in the Middle and Upper Susitna River drainage. 3. Characterize the genetic population structure of Chinook salmon from Upper Cook Inlet, with emphasis on spawning aggregates in the Middle and Upper Susitna River. 4. Examine the genetic variation among Chinook salmon populations from the Susitna River drainage, with emphasis on Middle and Upper River populations, for mixed-stock analyses (MSA). 5. If sufficient genetic variation is found for MSA, estimate the annual percent of juvenile Chinook salmon in selected Lower River habitats that originated in the Middle and Upper Susitna River in 2013 and 2014 (Figure 2-1). 3. STUDY AREA As established in the 2013 Genetics IP Section 2.2, the study area encompasses the Susitna River and its tributaries from Cook Inlet upstream to the Oshetna River confluence (RM 233.4 [PRM 261.3]; Figure 2). For baseline data related to stock-specific sampling, there was an emphasis on tributaries of the Middle and the Upper Susitna River. For assessing habitat use (juveniles) of fish originating from the Middle (RM 98 – 184 [PRM 102.4 – 187.1]) and Upper Susitna River (RM 184 – 233.4 [PRM 187.1 – 261.3]), tissue from juvenile Chinook salmon was collected in the Lower River (< RM 98 [PRM 102.4]). 4. Methods and Variances in 2013 AEA implemented the methods as described in the Study Plan with the exception of variances explained below (Section 4.5). INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 3 February 2014 Draft 4.1. Sample Collection For this study fish populations were defined using Waples and Gaggiotti’s (2006) definition: a group of individuals of the same species living in close enough proximity that any member of the group can potentially mate with any other member. Functionally, populations were represented by single or pooled collections following the “Pooling Collections into Populations” methods below. Based on field sampling from previous years (Tables 4-1 to 4-5), information gathered from the Catalog of Waters Important for the Spawning, Rearing or Migration of Anadromous Fishes ADF&G biologists selected possible sites where fish of each target Pacific salmon species might be spawning and generated idealized sample sizes for each site (Tables 4-1 to 4-5). ADF&G and AEA’s contractors made an intensive effort to collect these samples as outlined in the sections below. However, AEA recognized at the inception of this project (2013 Genetics IP) that it was unlikely to obtain the idealized sample size at all sites due to uncontrolled variables (i.e., numbers of fish at a spawning location, number of fish returning in 2013 and 2014, access limitations, water conditions, and catchability of the fish). Therefore, a column was added to Tables 4-1 to 4-5 labeled “Expected” that shows the number of fish that could reasonably be sampled at each site (or group of sites) in two years. AEA implemented the methods for sampling collection targets as described in the 2013 Genetics IP Section 4.2, with no variances. Collection targets , ranged between 0 and 200 individuals per species per location depending on the number of archived samples and prior knowledge about likely sample collection success (Tables 4-1 through 4-6). Samples were acquired from field collections performed as a part of this Study Plan (Studies 9.14), and from each of four interrelated studies: Study of Fish Distribution and Abundance in the Upper Susitna River (Study 9.5); Study of Fish Distribution and Abundance in the Middle and Lower Susitna River (Study 9.6); Salmon Escapement Study (Study 9.7); and Eulachon Run Timing, Distribution, and Spawning in the Susitna River Study (Study 9.16). All four interrelated studies provided samples from resident fish species collected in the course of their work (Table 4-6). Study 9.5 also provided samples of juvenile Chinook salmon (Table 4-1), and Study 9.7 provided samples from adult salmon from the Indian River and from the Middle River at Curry (detailed in Section 4.1.5). Sampling methods for this Study Plan are described below. Sampling methods for the four interrelated studies are described in those respective Initial Study Reports. Analysis of all samples will be integrated and reported in the Updated Study Report. 4.1.1. Adult Chinook salmon collections To address Objectives 3 and 4, tissue samples were to be collected during the study period from Chinook salmon spawning in drainages within Knik Arm and northwestern Cook Inlet, and within the Susitna River drainage. For drainages within Knik Arm and northwest Cook Inlet, this study was to augment the existing baseline by adding collections of up to 200 Chinook salmon from two tributaries from each area. For the Susitna River drainage, this project was to augment the existing baseline such that all tributaries were represented by at least 50 (and ideally 200) Chinook salmon. INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 4 February 2014 Draft Understanding the population structure of Chinook salmon collected above and below Devils Canyon will inform policymakers regarding the relatedness and isolation of spawning aggregates. Population structure of Chinook salmon will be measured at three different levels: within the set of individuals spawning above the canyon; among the groups of individuals spawning within the Susitna River watershed (with particular emphasis on the Middle River and Upper River); and in relationship to populations from nearby drainages in Upper Cook Inlet. These higher-level analyses will anchor the results and help provide a context for interpretation. Weekly survey flights were conducted from June 11 to September 15 in 2013 to determine the timing and locations for sampling all five species of salmon (Table 4-7) with the most intensive sampling of adult Chinook salmon occurring between July 15 and August 16 in 2013). Sampling crews were dispatched when and where Chinook salmon were observed in spawning habitats. Because Chinook salmon are generally spread out in streams and in lower abundance compared to other salmon species, multi-day sampling trips were required to get an adequate sample from each location (Table 4-1; Figure 4-5). During this time period, each of the three sampling crews attempted to collect samples from at least two locations per week with an average of 2.5 days per trip. The two extra days each week allowed crews to be relocated and resupplied with sampling gear, food, and other camping supplies, and acquire information from GCL staff for their next sampling location(s). During the intensive Chinook salmon sampling period, two crews were dedicated to sampling in the Susitna River. One crew was dedicated for sampling the Yentna River and northwestern Cook Inlet during the weeks of July 17 and 24 in 2013. Additional field staff collected Chinook salmon samples from locations along the road system in the Susitna River and Knik Arm from June 24 to July 19, 2013. Crews in the Susitna River had a helicopter (Robinson R-44 II; operated by Alpine Air Alaska, Inc.) on call for transport to and from sampling locations because of the large area to be sampled and short window of opportunity each year to collect Chinook salmon samples. The base of operations for the Alpine Air helicopter was Talkeetna. The Yentna River crew chartered helicopter (Enstrom F28F) flights, as needed, through Talaheim Lodge, based on the Talachulitna River. Chinook salmon were captured using either hook-and-line, seines, or gillnets depending on the size of the stream and where the fish were located. Upon capture, a single axillary process was clipped from each Chinook salmon and placed in a bottle of ethyl alcohol for preservation. For the two Chinook salmon sampled above Devils Canyon, additional paired samples/data were collected including scales, length (mid-eye to fork, to nearest 5 mm), sex, and GPS information (decimal degrees, to the nearest 0.001). Therefore, for these fish, axillary process and five scale samples were sampled into individually-labeled vials. Scales were sampled at a point along the diagonal line from the posterior insertion of the dorsal fin to the anterior insertion of the anal fin, two rows above the lateral line. Length, sex and GPS information was recorded on Rite-in-the- Rain® notebooks paired with the vial identifier. Fish were held in the water as much as possible while hooks were removed and samples were collected, and released immediately after the sample was placed in the bottle. If necessary, crews held the fish in the water to make sure they could swim before releasing them. Chinook salmon collections also occurred outside the three-week intensive sampling period as early as the second week of June and as late as the second week of August in 2013 (Table 4-8). INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 5 February 2014 Draft Collection trips during less intensive sampling periods were performed by two crews, but trip lengths were longer (approximately 4 days – one trip per crew per week) due to the lower availability of helicopter charters. Helicopter flights were chartered as needed, through Talaheim Lodge and Alpine Air, to access sites above Devils Canyon and sites not efficiently accessed by jet boat. Jet boats were used to access sites accessible from the road system in the Middle Susitna River. 4.1.2. Other adult salmon collections To address Objective 2, tissue samples were to be collected from 100 individuals (total archived and samples collected during the study period) from at least three spawning aggregates of pink, sockeye, chum, and coho salmon from each of the following drainages: 1) the Susitna River upstream of the Three Rivers Confluence (Middle Susitna River), 2) the Talkeetna River, and 3) the Chulitna River (Tables 4-2 to 4-5; Figures 4-1 to 4-4). Collections from adult pink, sockeye, chum, and coho salmon began on July 29 and continued through August 23, 2013 (Table 4-8). During the intensive Chinook salmon collection period, samples from these other salmon species were collected opportunistically by the two Susitna River crews. During the week of August 19, each of the two sampling crews was assigned to one of the following drainages to collect samples from at least three locations for each species: 1) the Talkeetna River, and 2) the Chulitna River. Collection locations and method of transport to sampling locations were determined after weekly survey flights. Odd-year pink salmon were present in the Middle Susitna River and Talkeetna River, but not in the Chulitna River. From the weeks of August 26 to September 9, poor weather limited the number of these survey flights (Table 4-7) and high water levels and turbid conditions precluded sampling (Table 4-8). Capture and sampling of salmon followed the methods used for adult Chinook salmon. Previously documented spawning time periods for each species in the Middle Susitna River, indicated below, were used as the general time periods for sampling trips (Thompson et al. 1986). • Pink salmon – last week of July to third week of August • Chum salmon – late-August to mid-September • Sockeye salmon – late-August to mid-September • Coho salmon – late-August to late-September 4.1.3. Juvenile Chinook salmon collections 4.1.3.1. Above Devils Canyon To address Objectives 3 and 4, tissue samples were to be collected from a target of 200 juvenile Chinook salmon during the study period at the Oshetna River and in each of Kosina, Fog, and Cheechako creeks. When possible in 2013, collections occurred at the same time as adult salmon collection trips. Collections in 2013 included 71 samples in Kosina Creek and three samples in the Oshetna River (Table 4-1); Cheechako and Fog creeks were not sampled. INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 6 February 2014 Draft Methods for capturing juvenile Chinook salmon in minnow traps followed Magnus et al. (2006). Cured salmon roe was used as bait and several minnow traps were set at each location. Minnow traps were checked at least once per day. Caudal fin tissue was collected from each juvenile Chinook salmon captured and placed in an individual 2 ml (0.07 oz) vial. Pelvic fins were too small to handle in the field, so caudal fins were sampled instead. Total length (snout-to-fork) was recorded for each sampled juvenile Chinook. 4.1.3.2. Lower River collections To address Objective 5, tissue samples were to be collected from 100 juvenile Chinook salmon during the study period from 16 sites across five mainstem habitat types in the Lower Susitna River (1,600 fish total). Samples of juvenile Chinook salmon collected in the Lower River were classified by habitat type to examine the potential for stock-specific variation in habitat type use. Habitat was classified according to mapping units and categories used in Characterization and Mapping of Aquatic Habitats Study (Study 9.9): main channel, side channel, side slough, backwater, tributary, and tributary mouth. Over the 2-year study, AEA will attempt to collect samples from up to three locations for each habitat type. Juvenile Chinook salmon in the Lower River were captured using the same methods as described for the juvenile Chinook collections above Devils Canyon. Minnow traps were checked at least once per day. Few new fish were captured between checks and the sampling objective (100 samples per location) was not met in 2013. Multiple locations were selected because the sampling objective could not be met at any of the locations initially selected. Tissue samples were collected using the same methods as described for the juvenile Chinook collections above Devils Canyon. 4.1.3.3. Species identification of juvenile collections Species identification was performed in the field using phenotypic characteristics (i.e. Pollard et al. 1997). The eight juvenile putative Chinook salmon collected below Devils Canyon will be analyzed with DNA markers to verify correct field species identification. All Pacific salmon captured above Devils Canyon were sampled and identified in the field as Chinook salmon. Species identification will be confirmed post-season using DNA. 4.1.4. Other species collections To address Objective 1, tissue samples were to be collected from up to 50 representative individuals during the study period from each of the resident fish species listed in Table 4-6, with an emphasis on fish collected in the Lower, Middle and Upper Susitna River. Samples of resident fish species were collected opportunistically while crews were collecting adult and juvenile salmon samples. Resident fish were identified to genus or species with a field key. A small piece of fin tissue was sampled from each fish and placed into a bottle or vial of ethyl alcohol for preservation. Samplers recorded on each bottle, or on datasheets for vial collections, from which of the following areas the samples were collected: 1) Chulitna River, 2) Talkeetna INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 7 February 2014 Draft River, 3) Upper Susitna River, 4) Middle Susitna River below Devils Canyon, 5) Middle Susitna River above Devils Canyon, or 6) Lower River. Tissues were placed in separate bottles for each species and area where they were collected. 4.1.5. Sampling coordination with other studies Tissue samples were also collected by four other studies in 2013: Study of Fish Distribution and Abundance in the Upper Susitna River (Study 9.5); Study of Fish Distribution and Abundance in the Middle and Lower Susitna River (Study 9.6); Salmon Escapement Study (Study 9.7); and Eulachon Run Timing, Distribution, and Spawning in the Susitna River Study (Study 9.16). Sampling kits and collection protocols were distributed to study leads in advance of the field season. During the 2013 field season, a series of 15 weekly field progress updates (June 28th through October 7th) were distributed to help coordinate sampling. These updates included upcoming sampling activities for each contractor, progress made towards sampling targets for each combination of species and study stratum, and a summary of sample deliveries to the GCL. In season, there was also frequent direct communication among ADF&G, the contractor liaison, and study leads designated for each interrelated study. Collection progress was updated using a database accessible to leads for studies 9.5, 9.6, 9.7, and 9.16. Once samples were delivered to the GCL, they were entered into ADFG’s LOKI database. Most of these samples were resident fish (Table 4-6) or juvenile Chinook salmon from above Devils Canyon (Table 4-1). As part of the Salmon Escapement Study (Study 9.7), AEA also collected samples from salmon at the Indian River weir, salmon radio-tagged at Curry (PRM 124-126), and salmon radio-tagged in the Lower River near the confluence with the Yentna River (PRM 33-34 of the Lower River, and RM 6 of the Yentna River). Sampling methods for all fish tissue samples provided from the interrelated studies are described in the respective ISRs. 4.1.6. Collection trip documentation Detailed notes were kept during each collection trip and then entered into the trip report database in the GCL Oracle database, LOKI, when crews returned to Anchorage (Appendix A). The following information was recorded for each trip: 1) trip logistical information, 2) GPS waypoints where fish were collected, 3) number of fish and species collected at each location, 4) notes on other fish species present, 5) life stage of observed fish, 6) fish habitat information, and 7) recommendations for future collection trips. Collection trip records were used post-season to submit Anadromous Waters Catalog nomination forms. 4.2. Tissue Storage AEA implemented the methods for tissue storage as described in Section 4.3 of the 2013 Genetics IP, with no variances. While in the field, tissue samples were preserved in ethyl alcohol in either a 125–500 ml (4.2-16.9 oz) bulk sample bottle for each location or individual 2 ml (0.07 oz) vials. After samples were received by the GCL, collection information was recorded in LOKI. For long-term storage, samples were preserved as follows: 1) placed into plastic plates and freeze-dried; 2) once dry, moisture-indicating desiccant beads were added and INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 8 February 2014 Draft the plate sealed completely with aluminum foil heat-activated tape; and 3) tissue samples stored at room temperature. 4.3. Laboratory Analysis Laboratory analysis began during the fourth quarter of 2013 (Figure 7.1), and methods were described in detail in the 2013 Genetics IP Section 4.4. 4.4. Data Retrieval and Quality Control Data retrieval and quality control will be accomplished as part of different ongoing activities, the first of which began in the fourth quarter of 2013. The 2013 Genetics IP Section 4.5 contains detailed descriptions of data retrieval and quality control methods. 4.5. Variances from Study Plan In 2013, there were no variances from the collection, storage and analysis methods described in the Genetic Baseline Study Plan; however, full access to all of the sampling sites in the 2013 Genetics IP was not available in 2013. The Study Plan for 2013 included sampling on streams that required access to Cook Inlet Regional Working Group (CIRWG) lands. Access was not granted to CIRWG lands in 2013, thereby fully or partially restricting sampling on some streams. Lack of access to CIRWG lands above or near Devils Canyon prevented potential sampling of Chinook salmon on Cheechako, Devil, Fog, Tsusena, and Watana creeks. Lack of access to CIRWG lands also prevented potential sampling at Portage and Prairie creeks for coho salmon, and reduced sampling at Prairie Creek for sockeye salmon. The study was designed to collect the target number of samples over multiple years. AEA will attempt to meet sampling targets for the locations on CIRWG lands in the next year of study if permission is granted to access these sites. Analysis of 2013 and 2014 collections will provide insight into whether there is a loss in power to test for stability in allele frequencies across years for Chinook salmon (testing between hypotheses 1a, 1b; Figure 2-1) and, if there is, the magnitude of this loss in power. 5. RESULTS 5.1. Sample Collection Sample collection results include all collections delivered to the GCL by September 15, 2013. 5.1.1. Adult Chinook salmon collections Survey flights to determine distribution and availability of Chinook salmon for sampling occurred from the week of June 8 to August 19 (Table 4-8). Fifty sites were surveyed from the air. AEA attempted to sample at 30 sites and successfully sampled at 27 sites (Table 4-1). Samples from 1,131 adult Chinook salmon were collected. Most of these samples were taken from the Susitna River drainage (1,073). Two of these samples were from above Devils Canyon. The remaining samples came from other drainages within upper Cook Inlet. INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 9 February 2014 Draft 5.1.2. Other adult salmon collections Survey flights to determine distribution and availability of other adult salmon species for sampling occurred from the week of July 29 to August 19 (Table 4-8). Of the 85 sites visited, 25 sites were surveyed from the air but sampling was not attempted (no fish or too few fish observed to justify sampling), 34 sites were sampled but no fish were captured, and 26 sites were successfully sampled for at least one adult salmon. Samples from 295 sockeye salmon were collected from 13 streams (Table 4-2). Samples from 641 chum salmon were collected from 14 streams (Table 4-3). Samples from 68 coho salmon were collected from 5 streams (Table 4-4). Samples from 1,041 pink salmon were collected from 12 streams (Table 4-5). 5.1.3. Juvenile Chinook salmon collections 5.1.3.1. Above Devils Canyon Sampling trips to collect juvenile Chinook salmon above Devils Canyon were conducted seven times in 2013. A total of 138 samples from juvenile Chinook salmon collected above Devils Canyon are available for analysis. Samples from 103 juvenile Chinook salmon were collected in 2013 from two tributaries above Devils Canyon (Oshetna River, n=32; Kosina Creek, n=71; Table 4-1). Of the 32 samples collected in the Oshetna River, 29 were acquired by ISR Study 9.5 (Study of Fish Distribution and Abundance in the Upper Susitna River). No samples were collected in Fog or Cheechako creeks in 2013. Archived tissues collected in 2012 are also available from Fog Creek (n=35). 5.1.3.2. Lower River collections Sampling trips to collect juvenile Chinook salmon in the Lower River were conducted four times in 2013. Samples from eight juvenile Chinook salmon were collected from the Lower River (Table 4-1). These samples were all collected from slough habitat on July 5, 2013 (Table 4-9). 5.1.4. Other species collections In 2013, opportunistic sampling for other (resident) species was conducted during all sampling trips and by the four interrelated AEA studies. In total, samples were collected from 1,255 fish, with sampling sites further broken into one of six potential strata (Table 4-6). The target sample size of 50 total fish per species reached for nine species (burbot, Dolly Varden, eulachon, Arctic grayling, slimy sculpin, three-spine stickleback, longnose sucker, rainbow trout, and round whitefish). No samples were collected for eight species (Alaska blackfish, Pacific lamprey, coastrange sculpin, Pacific staghorn sculpin, prickly sculpin, lake trout, Bering cisco, and lake whitefish). 5.1.5. Pacific salmon sampling coordination with other studies As part of the Salmon Escapement Study (Study 9.7), Pacific salmon were collected by AEA at the Indian River weir and from salmon radio-tagged at Curry. The 9 Chinook, 2 pink, 1 sockeye, and 13 chum salmon samples collected at the Indian River weir will be added to the baseline if needed. The 609 Chinook (including jacks), 232 coho, 201 chum, 199 pink, and 139 sockeye salmon samples taken from salmon radio-tagged at Curry will be used if the final spawning INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 10 February 2014 Draft locations can be determined from telemetry and sampling targets have not been met. Because of uncertainty about whether these samples will be added to the baseline, these collections are not reported in Tables 4-1 and 4-5. In addition, samples of Pacific salmon were collected at fishwheel sites as part of AEA-funded projects administered by the ADF&G Division of Sport Fish, but those samples were not delivered to GCL by September 15, 2013. 5.1.6. Collection trip documentation A total of 11 entries were made into the GCL Oracle database to document survey trips and 61 entries were made to document collection trips. 5.2. Tissue Storage For most of the collections (75 percent), samples were placed into bottles (multiple fish per container). In the remaining collections, samples were placed into vials (one fish per container). 5.3. Laboratory Analysis Laboratory and statistical analyses are ongoing and no results are available for inclusion in this Initial Study Report. Preliminary analyses will be used to inform consultations with USFWS and NMFS. Final analysis methods will be informed by these consultations. 5.4. Data Retrieval and Quality Control Data retrieval and quality control are ongoing and no results are available for inclusion in this Initial Study Report. 6. DISCUSSION The study was designed to achieve the target number of samples over the course of multiple years. With a few exceptions, sample collections of Pacific salmon species delivered to GCL through September 15, 2013 were sufficient to maintain progress toward study objectives (“Expected” columns in Tables 4-1 to 4-5). AEA will attempt to meet sampling targets for the locations on CIRWG lands in the next year of study if permission is granted to access these sites. However, even if sampling targets are met, limited access to these sites in 2013 may have reduced the power to test for stability in allele frequencies across years for Chinook salmon (testing between hypotheses 1a, 1b; Figure 2-1). Analysis of collections from 2013 and subsequent years will provide insight into whether there is a loss in power and, if there is, the magnitude of this loss in power. 6.1. Chinook Salmon Adults and Juveniles Above Devils Canyon Section 4.2 of the 2013 Genetics IP outlined sample collection in locations across the Susitna River basin. In 2013, Alaska Energy Authority was not granted access to Cook Inlet Regional INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 11 February 2014 Draft Working Group (CIRWG) lands to collect samples associated with this study. As a result AEA did not collect samples of adult salmon where they were observed on CIRWG lands from the air or through radio-tag tracking. For adult Chinook salmon, tributaries not accessed included Watana, Tsusena, Fog, Devil, and Cheechako creeks (all above or within Devils Canyon on the Susitna River). In addition, Portage Creek (below Devils Canyon on the Susitna River) and Prairie Creek (a Talkeetna River tributary) received a reduced sampling intensity due to lack of land access. Coho salmon adults were not sampled in Prairie and Portage creeks, and sampling effort for adult sockeye salmon was reduced. 6.2. Chinook Salmon Adults in the Middle River Below Devils Canyon Major strides were made toward collecting Chinook salmon in the Susitna drainage below Devils Canyon in 2013. Overall, 1,071 fish were collected from 23 sites. These numbers are close to what was anticipated for 2013 and 2014 combined (1,032 fish from 20 to 29 sites), although the geographic distribution of the collections differs. In the Yentna River, 202 fish were collected from three sites (project expected 390 fish from 9 sites over two years). In the Chulitna River, 444 fish were collected from 9 sites; (project expected 218 fish from 2 to 8 sites over two years). In the Middle River, below Devils Canyon, 95 fish were collected from 2 sites (project expected 134 fish from 2 to 6 sites over two years). In Talkeetna River, 246 fish were collected from 6 sites (project expected 131 fish from 2 to 6 sites over two years). Finally, from the Lower River, 84 fish were collected from 3 sites (project expected 159 fish from 5 to 9 sites over two years). 6.3. Chinook Salmon Adults Elsewhere Progress was made toward collecting Chinook salmon in the other drainages from Upper Cook Inlet in 2013. In the western side of Cook Inlet, 42 fish were collected from one site (study expected 235 fish from 4 sites over two years). In the Knik Arm, 16 fish were collected from two sites (study expected 181 fish from 5 to 7 sites over two years). Additional samples collected in 2013 are expected to arrive at the GCL from ADF&G Division of Sport Fish from weirs at three of these sites. 6.4. Chinook Salmon Juveniles – Lower River Despite four trips to collect juvenile Chinook salmon in the Lower River, only eight fish were sampled; all were from slough habitat on one sampling day (Table 4-9). Therefore, additional ADF&G staff, with vast experience annually capturing thousands of juvenile Chinook salmon from Southeast Alaska rivers, were invited to conduct a four-day training course on the Lower River during the week of September 23, 2013. This course was intended to train field crews on how to cure bait and bait traps and how to identify appropriate locations for setting traps and pulling seines following the methods outlined in Magnus et al. (2006). These techniques were applied late in the season in 2013 and will be applied during the next year of study. Results from these sampling efforts will be used to guide future sampling for juvenile Chinook salmon in the Lower River. INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 12 February 2014 Draft 6.5. Other Salmon Adults Fish were sometimes not found in sublocations where ADF&G expected to find them, but the study teams were able to capture fish in other sublocations within the targeted location. This was especially the case for pink and chum salmon, where less was known about the spawning distribution at the beginning of this study (Tables 4-3 and 4-5). For odd-year pink salmon, AEA sampled fewer than the targeted 300 fish within the Chulitna River (one fish), but met target sample numbers in the Middle Susitna River and Talkeetna River. These odd-year pink salmon do not appear to utilize spawning habitats in the Chulitna River. Odd-year pink salmon will not be available in 2014, so AEA’s ability to meet the target sample sizes for odd-year pink salmon in the Chulitna River will depend on the schedule of future sampling. Section 4.2.2 of the 2013 Genetics IP described a schedule of weekly survey flights between June 8 and September 23, and Section 4.2.3 described the plan for three sampling crews between late July and late September for adult salmon species other than Chinook salmon. Poor weather between August 19 and September 15, 2013 resulted in four fewer survey flights (Table 4-7) than planned. These cancelled survey flights represent 18 percent (4/22) of the survey flights planned for the season. This poor weather period also kept crews out of the field for three of the eight weeks (Table 4-8) called for in the 2013 Implementation Plan. This reduced survey effort came during the expected run timing of chum, sockeye, and coho salmon to their spawning grounds. For these three species, less progress was made towards achieving the sampling targets than expected in 2013, but it is anticipated that the sample targets can be achieved during the next year of study to meet study objectives (Table 4-5). 6.6. Other Fish Species Sample collections through September 15, 2013 were sufficient to attain or make progress towards study objectives for some resident species (Objective 1). Although the target sample size for each species was 50 fish for the entire Susitna River drainage, ADF&G also wanted to know roughly what part of the drainage the samples came from, and so asked field crews to reference each collection to one of six location “strata” in the drainage. ADF&G asked each field crew to collect up to 50 specimens from their strata to ensure the minimum for the drainage was met. Because crews worked concurrently in different strata, this meant 50 samples were able to be collected in multiple places for some species, and caused the drainage-wide target to be exceeded (e.g., rainbow trout; Table 4-6). The approved study methods include only opportunistic collection of resident fish species. Targets of 50 fish per species may not be met for those species that were not present during sampling, or were not susceptible to the sampling gear. No laboratory or statistical analyses are planned for genetic samples from resident species in this study. 6.7. Coordination with Other Studies Tissue samples from salmon radio-tagged by interrelated Study 9.7 provided a relatively high number of backup salmon samples in 2013. These samples will continue to be archived at the INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 13 February 2014 Draft GCL in the winter of 2013/2014; those fish whose final destinations can be determined will then be used to help fill any incomplete baselines at the end of this study. For resident fish species, the coordination with studies 9.5, 9.6, 9.7, and 9.16 allowed considerable success in 2013 (full or partial collection of samples for 12 of 20 species identified in the 2013 Study Plan). Species with no collections were likely either not in the study areas or were not vulnerable to the capture gear, making it unlikely that their collection targets can be reached with opportunistic sampling. 7. PLANS FOR COMPLETING THE STUDY [As explained in the cover letter to this draft ISR, AEA’s plan for completing this study will be included in the final ISR filed with FERC on June 3, 2014.] 8. LITERATURE CITED Alaska Energy Authority (AEA). 2012. Revised Study Plan: Susitna-Watana Hydroelectric Project FERC Project No. 14241. December 2012. Prepared for the Federal Energy Regulatory Commission by the Alaska Energy Authority, Anchorage, Alaska. http://www.susitna-watanahydro.org/study-plan. Magnus, D. L., D. Brandenberg, K. F. Crabtree, K. A. Pahlke, and S. A. McPherson. 2006. Juvenile salmon capture and coded wire tagging manual. Alaska Department of Fish and Game, Special Publications No. 06-31, Anchorage. Pollard, W. R., G. F., Hartman, C. Groot and P. Edgell. 1997. Field identification of coastal juvenile salmonids. Harbor Publishing. Thompson, F. M., S. N. Wick, and B. L. Stratton. 1986. Alaska Department of Fish and Game Susitna River Aquatics Studies Program. Report # 13, Volume 1: Adult Salmon Investigations May – October 1985. Alaska Power Authority, Anchorage, Alaska. Waples, R. S. and O. Gaggiotti. 2006. INVITED REVIEW: What is a population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity. Molecular ecology, 15(6): 1419-1439. INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 14 February 2014 Draft 9. TABLES INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 15 February 2014 Draft Table 4-1. Area, location, and sublocation of baseline samples of adult and juvenile Chinook salmon spawning aggregates for genetic analysis. Sample sizes show number of samples and sample years for collections already in the Gene Conservation Laboratory archives (Archived), number of samples to obtain the ideal archived sample size (Ideal), the anticipated number to be collected over the two years of this project based on past sampling effort and success and information from the Anadromous Waters Catalog and local biologists (Expected), progress made toward sampling targets this year (2013), and the resulting total sample size after combining the amount archived with the 2013 samples (Total). An “S” in the 2013 column indicates that a survey was performed but sampling was not attempted, a “-“ indicates that no survey was performed. Some of the expected numbers are for groups of locations. Sampling locations originally not included in the implementation plan have been included, and are indicated by an “n/a” ideal and expected value. New locations that are now included in grouped locations are sharing the expected value for their group. Map numbers (Map No.) correspond to location numbers on Figure 4-5. Sample sizes This project Area Location Sublocation Map No. Year(s) Collected (# archived) Ideal Expected (all years) 2013 Total Adult Chinook salmon West Side Cook Inlet Chuitna River 1 2008, 2009 (142) 200 58 - 142 Beluga River Coal Creek 2 2009, 2010, 2011 (120) 200 80 - 120 Theodore River 3 2010, 2011, 2012 (189) 200 11 42 231 Lewis River 4 2011, 2012 (86) 200 86 0 86 Yentna Drainage Clearwater Creek 5 2012 (25) 200 50 - 25 Red Creek 6 2012 (29) 200 58 82 111 Happy River 7 2012 (19) 200 38 S 19 Red Salmon Creek 8 2012 (12) 200 24 S 12 Hayes River 9 2012 (5) 200 10 45 50 Canyon Creek 10 2012 (32) 200 64 75 107 Talachulitna River 11 1995, 2008, 2010 (180) 200 20 - 180 Lake Creek Sunflower Creek 12 2009, 2011 (127) 200 71 S 127 Kahiltna River Peters Creek 13 2009, 2010, 2011, 2012 (110) 200 55 - 110 INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 16 February 2014 Draft Sample sizes This project Area Location Sublocation Map No. Year(s) Collected (# archived) Ideal Expected (all years) 2013 Total Susitna Drainage Chulitna River Middle Fork 14 2009, 2010, 2011 (182) 200 18 29 211 East Fork 15 200 200 63 415 West Fork 16 200 S Honolulu Creek 17 200 31 Pass Creek 18 n/a 33 Spink Creek 21 200 56 Byers Creek 19 200 54 Troublesome Creek 20 200 71 Tokositna River (Bunco Creek) 22 200 104 Tokosina River (Bunco Lake inlet stream) 23 n/a 3 Upper Susitna River Oshetna River 24 200 50 0 12 Kosina Creek 25 2012 (10) 200 2 Watana Creek 26 200 S Middle Susitna River above Devils Canyon Tsusena Creek 27 200 S Fog Creek 28 200 0 Devil Creek 30 200 S Chinook Creek 32 200 S INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 17 February 2014 Draft Sample sizes This project Area Location Sublocation Map No. Year(s) Collected (# archived) Ideal Expected (all years) 2013 Total Middle Susitna River below Devils Canyon Portage Creek 31 2009, 2010, 2011 (141) 200 59 25 166 Indian River 33 2012 (1) 200 75 70 71 Gold Creek 34 200 S Lane Creek 35 200 S Chase Creek 36 200 S Talkeetna River Prairie Creek 37 1995, 2008 (169) 200 31 33 202 no name creek #2 40 n/a 100 25 207 no name creek #1 39 n/a 71 upper mainstem 38 200 S Iron Creek 41 200 47 Disappointment Creek 42 200 64 Sheep River 43 200 S Larson Creek 44 200 S Chunilna Creek (Clear Creek) 45 2009, 2012 (130) 200 65 6 136 INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 18 February 2014 Draft Sample sizes This project Area Location Sublocation Map No. Year(s) Collected (# archived) Ideal Expected (all years) 2013 Total Lower Susitna River, upstream of Deshka River Montana Creek 46 2008, 2009, 2010 (218) 200 0 - 218 Birch Creek 47 200 50 S 84 Sheep Creek 48 200 22 North Fork Kashwitna River 49 200 12 Little Willow Creek 50 200 50 Willow Creek 51 1991,1997, 2005, 2009 (309) 200 0 - 309 Deshka River Moose Creek 52 1995, 2012 (103) 200 52 - 103 Deshka River weir 53 2005 (200) 200 0 - 200 Alexander Creek Sucker Creek 54 2011, 2012 (143) 200 57 - 143 Knik Arm Matanuska River Kings River 55 200 25 4 16 Granite Creek 56 200 12 Moose Creek 57 1995, 2008, 2009, 2012 (155) 200 45 - 155 Eagle River South Fork 58 2009, 2011, 2012 (73) 200 24 - 73 Meadow Creek 59 2009 (6) 200 12 - 6 Ship Creek 60 2009 (311) 200 0 - 311 Little Susitna River 61 2009, 2010 (125) 200 75 - 125 INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 19 February 2014 Draft Sample size This project Area Location Sublocation Map No. Year(s) Collected (for Archive) Ideal Expected (all years) 2013 Total Juvenile Chinook salmon Susitna Drainage Above Devils Canyon Oshetna River 24 2012 (35) 200 70 32* 138 Kosina Creek 25 200 71 Fog Creek 28 200 0 Cheechako Creek 29 200 - Susitna Drainage Lower River 5 habitat types n/a 1,600 1,600 8 8 (100 fish/habitat type times 3 or 4 collections) *29 juvenile Chinook salmon samples acquired by ISR Study 9.5 Fish Distribution and Abundance in the Upper Susitna River INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 20 February 2014 Draft Table 4-2. Location and sublocation of baseline samples of adult sockeye salmon spawning aggregates for genetic analysis. Sample sizes show number of samples and sample years for collections already in the Gene Conservation Laboratory archives (Archived), number of samples to obtain the ideal archived sample size (Ideal), the anticipated number to be collected over the two years of this project based on past sampling effort and success and information from the Anadromous Waters Catalog and local biologists (Expected), progress made toward sampling targets this year (2013), and the resulting total sample size after combining the amount archived with the new samples (Total). An “S” in the 2013 column indicates that a survey was performed but sampling was not attempted, a “- “ indicates that no survey was performed. Some of the expected numbers are for groups of locations. Sampling locations originally not included in the implementation plan have been included, and are indicated by an “n/a” ideal and expected value. New locations that are now included in grouped locations are sharing the expected value for their group. Map numbers (Map No.) correspond to location numbers on Figure 4-1. Sample sizes This project Area Location Sublocation Map No. Year(s) Collected (# archived) Ideal Expected (all years) 2013 Total Susitna River above three rivers confluence Chulitna River Middle Fork 2 100 100 0 0 East Fork 1 100 0 Pass Creek 5 n/a n/a 2 2 Spink Creek 4 2007, 2008 (126) 100 0 0 126 Byers Lake 3 1993, 2006, 2007 (243) 100 0 23 266 (Tokositna River) Sloughs 7 100 100 S 0 (Tokositna River) Swan Lake 8 2006, 2007, 2009 (109) 100 0 0 109 no-name creek 6 n/a n/a 6 6 Middle Susitna River below Devils Canyon Portage Creek 9 n/a 100 8 10 5th of July Creek 10 n/a 2 McKenzie Creek 11 100 0 Chase Creek 12 100 0 Mainstem sloughs above Three Rivers Confluence sloughs 8A,11, and 21 13 1995, 1996, 1997 (156) 100 0 80 236 slough 9 14 n/a 64 64 INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 21 February 2014 Draft Sample sizes This project Area Location Sublocation Map No. Year(s) Collected (# archived) Ideal Expected (all years) 2013 Total Susitna River above three rivers confluence Talkeetna River no-name creek 15 n/a 0 1 1 Stephan Lake 16 1993, 1994, 2007 (346) 100 0 - 346 Prairie Creek 17 n/a 0 2 2 Iron Creek 18 100 50 0 0 Disappointment Creek 19 n/a 0 11 11 Sloughs 20 1997 (79) 100 21 0 79 Sheep River 21 2008 (190) 100 0 S 190 Larson Lake - Eastern shore 23 2011 (90) 100 10 S 90 Larson Creek 22 1992, 1993 (200) 100 0 S 200 Larson Lake - outlet stream 24 2011 (126) 100 0 S 126 Chunilna Creek 25 100 100 18 18 Mama and Papa Bear Lakes 26 1997, 2007 (106) 100 0 75 181 Fish Creek 27 n/a 0 3 3 INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 22 February 2014 Draft Table 4-3. Location and sublocation of baseline samples of adult chum salmon spawning aggregates for genetic analysis. Sample sizes show number of samples and sample years for collections already in the Gene Conservation Laboratory archives (Archived), number of samples to obtain the ideal archived sample size (Ideal), the anticipated number to be collected over the two years of this project based on past sampling effort and success and information from the Anadromous Waters Catalog and local biologists (Expected), progress made toward sampling targets this year (2013), and the resulting total sample size after combining the amount archived with the new samples (Total). An “S” in the 2013 column indicates that a survey was performed but sampling was not attempted, a “- “ indicates that no survey was performed. Some of the expected numbers are for groups of locations. Sampling locations originally not included in the implementation plan have been included, and are indicated by an “n/a” ideal and expected value. New locations that are now included in grouped locations are sharing the expected value for their group. Map numbers (Map No.) correspond to location numbers on Figure 4-2. Sample sizes This project Area Location Sublocation Map No. Year(s) Collected (# archived) Ideal Expected (all years) 2013 Total Susitna River above Three Rivers Confluence Chulitna River Middle Fork 1 100 200 0 43 West Fork 2 100 S Byers Creek 3 100 18 Troublesome Creek 4 100 25 Spink Creek 5 2007, 2008 (45) 100 55 2 47 Tokositna River mainstem 6 100 50 S 0 Middle Susitna River below Devils Canyon Portage Creek 7 100 100 147 147 Indian River 8 100 100 123 123 Gold Creek 9 n/a n/a 5 5 sloughs above Three Rivers Confluence 10 1996 (103) 0 0 70 173 5th of July Creek 11 n/a n/a 34 34 4th of July Creek 12 n/a n/a 56 56 Lane Creek 13 n/a n/a 1 1 Whiskers Creek 14 n/a n/a 3 3 INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 23 February 2014 Draft Sample sizes This project Area Location Sublocation Map No. Year(s) Collected (# archived) Ideal Expected (all years) 2013 Total Talkeetna River upper mainstem 16 100 200 S 1 Disappointment Creek 17 100 S Sheep River 18 100 S Larson Creek 20 100 S Fish Creek 19 100 1 Sloughs 15 1995 (50) 100 50 20 70 Chunilna Creek 21 1993 (87) 100 13 136 223 INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 24 February 2014 Draft Table 4-4. Location and sublocation of baseline samples of adult coho salmon spawning aggregates for genetic analysis. Sample sizes show number of samples and sample years for collections already in the Gene Conservation Laboratory archives (Archived), number of samples to obtain the ideal archived sample size (Ideal), the anticipated number to be collected over the two years of this project based on past sampling effort and success and information from the Anadromous Waters Catalog and local biologists (Expected), progress made toward sampling targets this year (2013), and the resulting total sample size after combining the amount archived with the new samples (Total). An “S” in the 2013 column indicates that a survey was performed but sampling was not attempted, a “-“ indicates that no survey was performed. Some of the expected numbers are for groups of locations. Sampling locations originally not included in the implementation plan have been included, and are indicated by an “n/a” ideal and expected value. New locations that are now included in grouped locations are sharing the expected value for their group. Map numbers (Map No.) correspond to location numbers on Figure 4-3. Sample sizes This project Area Location Sublocation Map No. Year(s) Collected (# archived) Ideal Expected (all years) 2013 Total Susitna River above three rivers confluence Chulitna River Middle Fork 2 100 200 0 0 East Fork 1 100 0 Honolulu Creek 3 100 0 Byers Creek 4 100 0 Troublesome Creek 5 100 0 Spink Creek 6 2008 (38) 100 62 0 38 Tokositna River mainstem 7 100 100 S 0 Tokositna River (Bunco Creek) 8 100 0 Tokositna River (Swan Lake) 9 2009 (20) 100 80 0 20 Middle Susitna River Portage Creek 10 100 200 0 1 below Devils Canyon Indian River 11 100 1 Gold Creek 12 100 S McKenzie Creek 13 100 S Lane Creek 14 100 S Sloughs 15 100 75 2 2 Chase Creek 16 100 75 S 0 Whiskers Creek 17 100 75 62 62 INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 25 February 2014 Draft Sample sizes This project Area Location Sublocation Map No. Year(s) Collected (# archived) Ideal Expected (all years) 2013 Total Susitna River above three rivers confluence Talkeetna River upper mainstem 18 100 25 S 0 Prairie Creek 19 100 75 S 0 Sheep River 20 100 50 S 0 Larson Lake - outlet 21 2011 (84) 100 16 S 84 Chunilna Creek 22 100 75 2 2 Fish Creek 23 n/a n/a 1 1 INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 26 February 2014 Draft Table 4-5. Location and sublocation of baseline samples of adult pink salmon spawning aggregates for genetic analysis. Sample sizes show number of samples and sample years for collections already in the Gene Conservation Laboratory archives (Archived), number of samples to obtain the ideal archived sample size (Ideal), the anticipated number to be collected over the two years of this project based on past sampling effort and success and information from the Anadromous Waters Catalog and local biologists (Expected), progress made toward sampling targets this year (2013), and the resulting total sample size after combining the amount archived with the new samples (Total). An “S” in the 2013 column indicates that a survey was performed but sampling was not attempted, a “-“ indicates that no survey was performed. Some of the expected numbers are for groups of locations. Sampling locations originally not included in the implementation plan have been included, and are indicated by an “n/a” ideal and expected value. New locations that are now included in grouped locations are sharing the expected value for their group. Map numbers (Map No.) correspond to location numbers on Figure 4-4. Sample sizes This project Area Location Sublocation Map No. Year(s) Collected (for Archive) Ideal Expected (all years) 2013 Total Susitna River above three rivers confluence Chulitna River Middle Fork 1 100 100 0 1 Spink Creek 3 100 0 Troublesome Creek 2 100 0 no name creek 4 n/a 1 Middle Susitna River below Devils Canyon Portage Creek 5 100 50 136 136 Indian River 6 100 100 114 114 Gold Creek 7 100 50 106 446 5th of July Creek 8 n/a 2 4th of July Creek 9 n/a 107 slough 9 10 n/a 116 McKenzie Creek 11 100 0 Lane Creek 12 100 115 Chase Creek 13 100 0 Whiskers Creek 14 100 15 INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 27 February 2014 Draft Sample sizes This project Area Location Sublocation Map No. Year(s) Collected (for Archive) Ideal Expected (all years) 2013 Total Talkeetna River upper mainstem 15 100 25 0 0 Disappointment Creek 16 n/a 0 127 127 Sheep River 17 100 25 0 0 Larson Creek 18 100 100 0 0 Chunilna Creek 19 100 100 101 101 Fish Creek 20 n/a 0 101 101 INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 28 February 2014 Draft Table 4-6. Resident and non-salmon anadromous fish species targeted for genetic tissue sampling in the Susitna River and samples sizes collected in 2013. Sample collections are reported for the Gene Conservation Laboratory (GCL), interrelated studies (other), and the combined total (N). Species Target sample size (total) Collection Strata Total Collected Upper Susitna River Middle Susitna River above Devils Canyon Middle Susitna River below Devils Canyon Lower Susitna River Talkeetna River Chulitna River GCL other studies N GCL other studies N GCL other studies N GCL other studies N GCL other studies N GCL other studies N Blackfish, Alaska 50 0 0 0 0 0 0 0 Burbot 50 0 0 4 4 2 102 104 0 0 108 Dolly Varden 50 1 1 3 3 5 5 4 3 7 35 35 0 51 Eulachon 50 0 0 0 283 283 0 0 283 Grayling, Arctic 50 17 17 21 21 45 14 59 7 4 11 5 5 3 3 116 Lamprey, Arctic* n/a 9 9 9 Lamprey, Pacific 50 0 0 0 0 0 0 0 Pike, northern 50 0 0 0 16 16 0 0 16 Sculpin, coastrange 50 0 0 0 0 0 0 0 Sculpin, Pacific staghorn 50 0 0 0 0 0 0 0 Sculpin, prickly 50 0 0 0 0 0 0 0 Sculpin, slimy 50 15 15 40 100 140 0 52 52 0 0 207 Stickleback, ninespine 50 0 0 0 7 7 0 0 7 INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 29 February 2014 Draft Species Target sample size (total) Collection Strata Total Collected Upper Susitna River Middle Susitna River above Devils Canyon Middle Susitna River below Devils Canyon Lower Susitna River Talkeetna River Chulitna River GCL other studies N GCL other studies N GCL other studies N GCL other studies N GCL other studies N GCL other studies N Stickleback, threespine 50 0 0 0 50 92 142 0 0 142 Sucker, longnose 50 0 0 5 5 1 102 103 0 0 108 Trout, lake 50 0 0 0 0 0 0 0 Trout, rainbow 50 0 1 1 40 40 40 7 47 19 19 23 2 3 130 Whitefish, Bering cisco 50 0 0 0 0 0 0 0 Whitefish, humpback 50 3 3 0 0 0 0 0 3 Whitefish, lake 50 0 0 0 0 0 0 0 Whitefish, round 50 2 2 0 57 9 66 0 1 1 6 6 75 * Collected, but not on original list of target species INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 30 February 2014 Draft Table 4-7. Summary of survey flights conducted during 2013. Surveys were performed throughout the summer of 2013 in order to determine potential sampling locations for five salmon species (Chinook, sockeye, pink, chum, and coho salmon). X’s indicate the occurrence of a survey flight in a given collection strata (Figure 3-1) on a certain date. Survey flight number 17 shows no X’s because the survey was cancelled due to poor survey conditions. Collection strata Survey # Date Upper Susitna River Middle Susitna above Devils Canyon Middle Susitna below Devils Canyon Lower Susitna River Talkeetna River Chulitna River West Side Cook Inlet Yentna Drainage Knik Arm 1 6/11/2013 X X X X X 2 7/8/2013 X X X 3 7/9/2013 X X X X 5 7/15/2013 X X X 6 7/16/2013 X X 7 7/17/2013 X 8 7/22/2013 X X X X 9 7/23/2013 X X 10 7/24/2013 X 11 7/29/2013 X X X X 12 7/30/2013 X X 13 8/5/2013 X X X 14 8/6/2013 X X X X X 15 8/12/2013 X 16 8/13/2013 X X X 17 8/19/2013 18 8/26/2013 X X 19 9/15/2013 X X INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 31 February 2014 Draft Table 4-8. Genetic sampling effort through time by river area for adult salmon species in 2013. Salmon species sampled are reported by week and strata. X’s indicate where sampling occurred in each week of the Project field season for all salmon species, and for sampling locations where Chinook salmon were the only target species. Species sampled: Chinook (K), sockeye (S), pink (P), chum (Ch), and coho (Co) salmon. Sampling occurred from 6/8/2013 through 9/15/2013. Collection Strata Area sampled (all salmon species) Area sampled (Chinook salmon only) Week of Species sampled Talkeetna Chulitna Middle Susitna below Devils Canyon Lower Susitna Middle Susitna above Devils Canyon Yentna Knik West 6/8-25/2013 K x 6/24/2013 K x x 7/1/2013 K x x x 7/8/2013 K x x x 7/15/2013 K x x x 7/22/2013 K x x x x 7/29/2013 K, S, Ch, P, Co, x x x x 8/5/2013 K,S, Ch, P,Co x x x x 8/12/2013 K, S, Ch, P, Co x x x x 8/19/2013 S, Ch, P x x 8/26/2013 * 9/2/2013 * 9/9/2013 * * Sampling efforts disrupted by adverse weather conditions. INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 32 February 2014 Draft Table 4-9. Juvenile Chinook salmon tissue collections across five habitat types in the Lower Susitna River, through September 15, 2013. Collection numbers of juvenile Chinook salmon tissues are reported for 16 collection sites over 5 different habitat types (main channel, backwater, braid, channel edge, and slough) in the Lower Susitna River. Totals per stratum are reported (totals). Habitat Type Main channel Braid Channel edge Slough Backwater collection site number collection site number collection site number collection site number collection site number DATE 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 7/5/2013 8 Totals: 8 INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 33 February 2014 Draft Table 4-10. Metadata and location of Chinook salmon samples collected above Devils Canyon. Length (in millimeters) and sex were determined for Chinook salmon sampled above Devils Canyon on August 6, 2013. Creek name, latitude, and longitude are also reported for these data. Fish # Date Length Sex Creek Latitude/Longitude 1 8/6/2013 980 M Kosina 62.701/ -147.986 2 8/6/2013 575 F Kosina 62.633/ -148.031 DRAFT INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 34 Draft: March 2013 10. FIGURES Figure 2-1. A generalized flow chart to distinguish among hypotheses of population structure for Chinook salmon collected over spawning habitat above Devils Canyon in the Middle and Upper Susitna River. Only a self-sustaining population (Hypothesis 1a) will potentially result in genetic variation suitable for mixed-stock analysis for estimating the proportion of juvenile Chinook salmon mixtures collected in the Middle and Lower Susitna River that originate from above Devils Canyon. DRAFT INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 35 Draft: March 2013 Figure 3-1. Collection strata for samples collected for genetic archive and/or analysis. DRAFT INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 36 Draft: March 2013 Figure 4-1. Baseline sampling locations for adult sockeye salmon. Circles indicate the number of samples in the Gene Conservation Laboratory archives. Numbers correspond to map numbers on Table 4-3. DRAFT INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 37 Draft: March 2013 Figure 4-2. Baseline sampling locations for adult chum salmon. Circles indicate the number of samples in the Gene Conservation Laboratory archives. Numbers correspond to map numbers on Table 4-4. DRAFT INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 38 Draft: March 2013 Figure 4-3. Baseline sampling locations for adult coho salmon. Circles indicate the number of samples in the Gene Conservation Laboratory archives. Numbers correspond to map numbers on Table 4-5. DRAFT INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 39 Draft: March 2013 Figure 4-4. Baseline sampling locations for adult pink salmon. Circles indicate the number of samples in the Gene Conservation Laboratory archives. Numbers correspond to map numbers on Table 4-6. DRAFT INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Page 40 Draft: March 2013 Figure 4-5. Baseline sampling locations for adult and juvenile (inset) Chinook salmon. Circles indicate the number of samples in the Gene Conservation Laboratory archives. Numbers correspond to map numbers in Table 4-2. The Lower Susitna River (below project river mile (PRM) 102.4), Middle River (RM 102.4- 187.1) and Upper River (RM 187.1-235.1) segments are highlighted with the proposed dam at PRM 187.1. DRAFT INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 February 2014 APPENDIX A: TEMPLATE FOR COLLECTION TRIP REPORTS DRAFT INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Appendix A – Page 1 February 2014 LOKI Trip Report Form Trip Start Date Trip End Date Trip Name Charter Transportation Lodging Report Date Report Author Waypoint Name: Potential Access: camp/survey/collection latitude longitude waypoint comments Waypoint Name: Potential Access: camp/survey/collection latitude longitude waypoint comments Waypoint Name: Potential Access: camp/survey/collection latitude longitude waypoint comments Waypoint Name: Potential Access: camp/survey/collection latitude longitude waypoint comments Waypoint Name: Potential Access: camp/survey/collection latitude longitude waypoint comments Waypoint Name: Potential Access: DRAFT INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14) Susitna-Watana Hydroelectric Project Alaska Energy Authority FERC Project No. 14241 Appendix A – Page 2 February 2014 camp/survey/collection latitude longitude waypoint comments TRIP COMMENTS ON REVERSE SIDE TRIP COMMENTS